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Aspergillus niger Phytase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IHP PDB ENTRY 1IHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 25% (w/v) PEG 3350, 0.4M ammonium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.066 α = 90 b = 87.457 β = 110.98 c = 82.185 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r BEAMLINE OPTICS 2009-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953715 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 76.74 96.6 0.138 6.6 3.5 35613 35613 -3 -3 35.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.53 99.8 0.542 2.4 3.5 5338
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IHP 2.4 66.36 -1 -1 33827 33827 1770 96.55 0.21825 0.21825 0.21528 0.2139 0.27548 0.271 RANDOM 26.967
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.3 -3.04 0.08 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.047 r_dihedral_angle_4_deg 18.61 r_dihedral_angle_3_deg 16.495 r_dihedral_angle_1_deg 6.722 r_scangle_it 3.247 r_scbond_it 2.023 r_angle_refined_deg 1.68 r_mcangle_it 1.33 r_mcbond_it 0.727 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.047 r_dihedral_angle_4_deg 18.61 r_dihedral_angle_3_deg 16.495 r_dihedral_angle_1_deg 6.722 r_scangle_it 3.247 r_scbond_it 2.023 r_angle_refined_deg 1.68 r_mcangle_it 1.33 r_mcbond_it 0.727 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6777 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 84
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling